scROAD: single-cell Regulatory Occupancy Analysis of Dynamics

Introduction

This the tutorial for running Cicero and TOBIAS packages on single cell ATAC data generated from cellranger.

The complete code has already been shared in the paper: scMultiomics_identifies_shared_and_distinct_pathways_in_Picks_and_Alzheimers_disease GitHub. Here is a more organized tutorial, and shortly we will provide a wrapper package to summarize the in-between steps for user eaiser to handle the data between all those tools .

To support the paper, we have built a database for checking the prediction of TF binding difference between two dementia and their age-matched control; and a package for easy running multiple code before/during TOBIAS and integrating co-accessibility results from Cicero.

scROAD

scROAD stands for:

1. single-cell Regulatory Occupancy Analysis of Dynamics:
   This highlights the analytical framework and methodology used for studying transcription factor occupancy and regulatory changes in single-cell data.

2. Single-cell Regulatory Occupancy Archive in Dementia:
   This emphasizes the curated database or archive for dementia-related research, housing single-cell regulatory data for further exploration.

These dual meanings reflect the comprehensive scope of scROAD, addressing both the analytical methods and the accessible resource for the scientific community.

How to cite

Bentsen, M., Goymann, P., Schultheis, H. et al. ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation. Nat Commun 11, 4267 (2020). https://doi.org/10.1038/s41467-020-18035-1

Shi, Das & Morabito et al. Single-nucleus multi-omics identifies shared and distinct pathways in Pick’s and Alzheimer’s disease.

Contributors

Zechuan Shi @rootze from Swarup lab at UCI

Samuel Morabito @smorabit from Swarup lab at UCI

Software, Algorithms, and Resources

Zechuan Shi @rootze created analysis documents that combine code

Programming software:

• R v4.1.1 and above
• Python v3.6 and above

Tools_Software:

• Signac (v1.9.0)
• ArchRtoSignac (v1.0.4)
• Seurat (v4.4.0)
• Cicero ()
• TOBIAS (v0.14.0)

Getting help

In case of any issues/questions/comments, please check out the Issues. Otherwise, please write an issue for any questions here.